Energetic Self-Folding Mechanism in α-Helices

Abstract

A novel energetic route driving the folding of a polyalanine peptide from an extended conformation to its α-helix native conformation is described, supported by a new method to compute mean potential energy surfaces accurately in terms of the dihedral angles of the peptide chain from extensive molecular dynamics simulations. The energetic self-folding (ESF) route arises specifically from the balance between the intrinsic propensity of alanine residues toward the α_R conformation and two, opposite, effects: the destabilizing interaction with neighbor residues and the stabilizing formation of native hydrogen bonds, with the latter being dominant for large peptide lengths. The ESF mechanism provides simple but robust support to the nucleation-elongation or zipper models and offers a quantitative energetic funnel picture of the folding process. The mechanism is validated by the reasonable agreement between the computed folding energies and the experimental values.